I
Isaac Ho
Researcher at Joint Genome Institute
Publications - 12
Citations - 6641
Isaac Ho is an academic researcher from Joint Genome Institute. The author has contributed to research in topics: Genome & Sequence assembly. The author has an hindex of 11, co-authored 12 publications receiving 6292 citations. Previous affiliations of Isaac Ho include Agency for Science, Technology and Research & United States Department of Energy.
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Journal ArticleDOI
The draft genome of Ciona intestinalis : insights into chordate and vertebrate origins
Paramvir S. Dehal,Yutaka Satou,Robert K. Campbell,Jarrod Chapman,Bernard M. Degnan,Anthony W. De Tomaso,Brad Davidson,Anna Di Gregorio,Maarten D. Sollewijn Gelpke,David Goodstein,Naoe Harafuji,Kenneth E. M. Hastings,Isaac Ho,Kohji Hotta,Wayne Huang,Takeshi Kawashima,Patrick Lemaire,Diego Martinez,Ian A. Meinertzhagen,Simona Necula,Masaru Nonaka,Nik Putnam,Sam Rash,Hidetoshi Saiga,Masanobu Satake,Astrid Terry,Lixy Yamada,Hong Gang Wang,Satoko Awazu,Kaoru Azumi,Jeffrey L. Boore,Margherita Branno,Stephen T. Chin-Bow,Rosaria DeSantis,Sharon A. Doyle,Pilar Francino,David N. Keys,David N. Keys,Shinobu Haga,Hiroko Hayashi,Kyosuke Hino,Kaoru S. Imai,Kazuo Inaba,Shungo Kano,Shungo Kano,Kenji Kobayashi,Mari Kobayashi,Byung In Lee,Kazuhiro W. Makabe,Chitra Manohar,Giorgio Matassi,Mónica Medina,Yasuaki Mochizuki,Steve Mount,Tomomi Morishita,Sachiko Miura,Akie Nakayama,Satoko Nishizaka,Hisayo Nomoto,Fumiko Ohta,Kazuko Oishi,Isidore Rigoutsos,Masako Sano,Akane Sasaki,Yasunori Sasakura,Eiichi Shoguchi,Tadasu Shin-I,Antoinetta Spagnuolo,Didier Y.R. Stainier,Miho Suzuki,Olivier Tassy,Naohito Takatori,Miki Tokuoka,Kasumi Yagi,Fumiko Yoshizaki,Shuichi Wada,Cindy Zhang,P. Douglas Hyatt,Frank W. Larimer,Chris Detter,Norman A. Doggett,Tijana Glavina,Trevor Hawkins,Paul G. Richardson,Susan Lucas,Yuji Kohara,Michael Levine,Nori Satoh,Daniel S. Rokhsar,Daniel S. Rokhsar +89 more
TL;DR: A draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis, is generated, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development.
Journal ArticleDOI
Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes
Samuel Aparicio,Jarrod Chapman,Elia Stupka,Nik Putnam,Jer Ming Chia,Paramvir S. Dehal,Alan Christoffels,Sam Rash,Shawn Hoon,Arian F.A. Smit,Maarten D. Sollewijn Gelpke,Jared C. Roach,Tania Oh,Isaac Ho,Marie Wong,Chris Detter,Frans Verhoef,Paul Predki,Alice Tay,Susan Lucas,Paul G. Richardson,Sarah Smith,Melody S. Clark,Yvonne J. K. Edwards,Norman A. Doggett,Andrey Zharkikh,Sean V. Tavtigian,Dmitry Pruss,Mary Barnstead,Cheryl Evans,Holly Baden,Justin Powell,Gustavo Glusman,Lee Rowen,Leroy Hood,Y. H. Tan,Greg Elgar,Trevor Hawkins,Byrappa Venkatesh,Daniel S. Rokhsar,Sydney Brenner +40 more
TL;DR: The Fugu rubripes genome has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds as discussed by the authors.
Journal ArticleDOI
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina).
Diego Martinez,Diego Martinez,Randy M. Berka,Bernard Henrissat,Markku Saloheimo,Mikko Arvas,Scott E. Baker,Jarod Chapman,Olga Chertkov,Pedro M. Coutinho,Dan Cullen,Etienne Danchin,Igor V. Grigoriev,Paul Harris,Melissa Jackson,Christian P. Kubicek,Cliff Han,Isaac Ho,Luis F. Larrondo,Alfredo Lopez de Leon,Jon K. Magnuson,Sandy Merino,Monica Misra,Beth Nelson,Nicholas H. Putnam,Barbara Robbertse,Asaf Salamov,Monika Schmoll,Astrid Terry,Nina Thayer,Ann Westerholm-Parvinen,Conrad L. Schoch,Jian Yao,Ravi D. Barabote,Mary Anne Nelson,Chris Detter,David Bruce,Cheryl R. Kuske,Gary Xie,Paul G. Richardson,Daniel S. Rokhsar,Susan Lucas,Edward M. Rubin,Nigel Dunn-Coleman,Michael Ward,Thomas Brettin +45 more
TL;DR: This work assembled 89 scaffolds to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models, providing a roadmap for constructing enhanced T.Reesei strains for industrial applications such as biofuel production.
Journal ArticleDOI
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Keith Bradnam,Joseph Fass,Anton Alexandrov,Paul Baranay,Michael Bechner,Inanc Birol,Sébastien Boisvert,Jarrod Chapman,Guillaume Chapuis,Guillaume Chapuis,Rayan Chikhi,Rayan Chikhi,Hamidreza Chitsaz,Wen-Chi Chou,Jacques Corbeil,Cristian Del Fabbro,T. Roderick Docking,Richard Durbin,Dent Earl,Scott J. Emrich,Pavel Fedotov,Nuno A. Fonseca,Ganeshkumar Ganapathy,Richard A. Gibbs,Sante Gnerre,Elenie Godzaridis,Steve Goldstein,Matthias Haimel,Giles Hall,David Haussler,Joseph B. Hiatt,Isaac Ho,Jason T. Howard,Martin Hunt,Shaun D. Jackman,David B. Jaffe,Erich D. Jarvis,Huaiyang Jiang,Sergey Kazakov,Paul J. Kersey,Jacob O. Kitzman,James R. Knight,Sergey Koren,Tak-Wah Lam,Dominique Lavenier,Dominique Lavenier,François Laviolette,Yingrui Li,Zhenyu Li,Binghang Liu,Yue Liu,Ruibang Luo,Iain MacCallum,Matthew D. MacManes,Nicolas Maillet,Sergey Melnikov,Bruno Vieira,Delphine Naquin,Zemin Ning,Thomas D. Otto,Benedict Paten,Octávio S. Paulo,Adam M. Phillippy,Francisco Pina-Martins,Michael Place,Dariusz Przybylski,Xiang Qin,Carson Qu,Filipe J. Ribeiro,Stephen Richards,Daniel S. Rokhsar,Daniel S. Rokhsar,J. Graham Ruby,J. Graham Ruby,Simone Scalabrin,Michael C. Schatz,David C. Schwartz,Alexey Sergushichev,Ted Sharpe,Timothy I. Shaw,Jay Shendure,Yujian Shi,Jared T. Simpson,Henry Song,Fedor Tsarev,Francesco Vezzi,Riccardo Vicedomini,Jun Wang,Kim C. Worley,Shuangye Yin,Siu-Ming Yiu,Jianying Yuan,Guojie Zhang,Hao Zhang,Shiguo Zhou,Ian F Korf +95 more
TL;DR: The Assemblathon 2 as mentioned in this paper presented a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and a snake) from 21 participating teams.
Journal ArticleDOI
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Keith Bradnam,Joseph Fass,Anton Alexandrov,Paul Baranay,Michael Bechner,Inanc Birol,Sébastien Boisvert,Jarrod Chapman,Guillaume Chapuis,Guillaume Chapuis,Rayan Chikhi,Rayan Chikhi,Hamidreza Chitsaz,Wen-Chi Chou,Jacques Corbeil,Cristian Del Fabbro,Roderick R. Docking,Richard Durbin,Dent Earl,Scott J. Emrich,Pavel Fedotov,Nuno A. Fonseca,Ganeshkumar Ganapathy,Richard A. Gibbs,Sante Gnerre,Elenie Godzaridis,Steve Goldstein,Matthias Haimel,Giles Hall,David Haussler,Joseph B. Hiatt,Isaac Ho,Jason T. Howard,Martin Hunt,Shaun D. Jackman,David B. Jaffe,Erich D. Jarvis,Huaiyang Jiang,Sergey Kazakov,Paul J. Kersey,Jacob O. Kitzman,James R. Knight,Sergey Koren,Tak-Wah Lam,Dominique Lavenier,Dominique Lavenier,Dominique Lavenier,François Laviolette,Yingrui Li,Zhenyu Li,Binghang Liu,Yue Liu,Ruibang Luo,Iain MacCallum,Matthew D. MacManes,Nicolas Maillet,Nicolas Maillet,Sergey Melnikov,Delphine Naquin,Delphine Naquin,Zemin Ning,Thomas D. Otto,Benedict Paten,Octávio S. Paulo,Adam M. Phillippy,Francisco Pina-Martins,Michael Place,Dariusz Przybylski,Xiang Qin,Carson Qu,Filipe J. Ribeiro,Stephen Richards,Daniel S. Rokhsar,Daniel S. Rokhsar,J. Graham Ruby,J. Graham Ruby,Simone Scalabrin,Michael C. Schatz,David C. Schwartz,Alexey Sergushichev,Ted Sharpe,Timothy I. Shaw,Jay Shendure,Yujian Shi,Jared T. Simpson,Henry Song,Fedor Tsarev,Francesco Vezzi,Riccardo Vicedomini,Bruno Vieira,Jun Wang,Kim C. Worley,Shuangye Yin,Siu-Ming Yiu,Jianying Yuan,Guojie Zhang,Hao Zhang,Shiguo Zhou,Ian F Korf +98 more
TL;DR: The Assemblathon 2 as discussed by the authors presented a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and a snake) from 21 participating teams.